RetrogeneDB ID: retro_ptri_1

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 19:10023693..10024743(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0019s08510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0006s01590
• Aliases: None
• Description: None

Sequence

>retro_ptri_1
AACAAAACTAAGATTACTCCTGTCGAAATAGTACGAGAAACTCAGAGGCTCTTGTTGTGTATTAGTTCTGATCATGGTTT
AAAACAAGAAGAGAAGAAGAAGAAGGCAGATTTAAAACAAGAAAACAAGGCGGCGGCAGCGCTGGCTAAAAATATCAGGG
CTTTGAAGTCAATTGCTTATGGCAATGATGAGTCTTCTGCAGTCTCAAGAGCCTGTGCACAATTGACAGAGGAGTTCTTC
AGAGAGAACACACTTCCTCTCCTCATCGTCTGTCTTCCGAAATTGACCTTGGAGGCCCAGAGAGATGCCACTCAAGTTGT
TGCAAATCTACTACGGCATAAAGTTCAGTCCCGGTTGATTGCATCAGAATACTTGGAGAAAAATACTGATGTTCTTGATC
TTTTGGTAGCAGGTTGTGGAAACATGGACATGGCTATCCAATACGGTGAAATTCTAAGGGCGTGTCTGCGTCACCAGAGT
GCTGCGAGATATGTTCTTGAATCACCAGCACATCTGAAGAAGTTTTTTGATTATATACAGCTTCGGTATTTCGACATTGC
CTCAAATGCCGCCTTAACGCTCAAGGAACTATTGACAAGGCATAAATATTCTCTAGTTCCTGAATTTCTTTCTAAGAACT
ATGAATGGTTCTTCGCGGATTTTAATTCGAAGCTGCTGGAATCCTCTGATTATTTTACAAGAATACAAGCTACCAAGCTG
CTGGGACACATGCTGTTGGATCACTCTAATTCAGCTGTGATGGCACGATACGTGAGCTCGAGGAACAATCTGAGGATTGT
TATGAATCTCCTCAGGGATTCAAGTAAGTGCATCCGGATAAAGGCATTTCATGTTTTCAAGCTCTTCGCTGCAAATCAAA
ATAGGCCTTTCGACATCATCACCGTGCTTGTGGCAAACAGGAGCAAGCTTCTTCGTTTCCTTGCTGATTTCAAGACAGAT
AAAGAGGATGAATGTTTCGAGGCAGACAAAGCTCAAGTCATGAAAGAAATAGTTGCCCTCGATCCTAGAGATCATGAGAG
CTATGAGTGA

Alignment

ORF - retro_ptri_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.17 %
• Parental protein coverage: 90.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDSKREEKMAE-LAKNTRELKSILYGNSESEPVSEACAQLTQEFFRENTLRLLIICLPKLNLETRKDATQ
          .D.K.E.K.A..LAKN.R.LKSI.YGN.ES..VS.ACAQLT.EFFRENTL.LLI.CLPKL.LE...DATQ
Retrocopy ADLKQENKAAAALAKNIRALKSIAYGNDESSAVSRACAQLTEEFFRENTLPLLIVCLPKLTLEAQRDATQ

Parental  VVANLQRQQVNSRLIASDYLEKNTDLLDILIAGYENTDMALHYGVMLKECIRHQSVARYVLESP-HVKKF
          VVANL.R..V.SRLIAS.YLEKNTD.LD.L.AG..N.DMA..YG..L..C.RHQS.ARYVLESP.H.KKF
Retrocopy VVANLLRHKVQSRLIASEYLEKNTDVLDLLVAGCGNMDMAIQYGEILRACLRHQSAARYVLESPAHLKKF

Parental  FDYIQLPNFDISADAAATFKELLTRHK-STVAEFLSKNYDWFFAEFNSKLLESTNYITRRQSIKLLGDML
          FDYIQL..FDI...AA.T.KELLTRHK.S.V.EFLSKNY.WFFA.FNSKLLES..Y.TR.Q..KLLG.ML
Retrocopy FDYIQLRYFDIASNAALTLKELLTRHKYSLVPEFLSKNYEWFFADFNSKLLESSDYFTRIQATKLLGHML

Parental  LDRSNAVVMTRYVSSRDNLRILMNLLRESSKSIQTEAFHVFKLFVANQNKPPDIVSILVANRSKLLRLLA
          LD.SN..VM.RYVSSR.NLRI.MNLLR.SSK.I...AFHVFKLF.ANQN.P.DI...LVANRSKLLR.LA
Retrocopy LDHSNSAVMARYVSSRNNLRIVMNLLRDSSKCIRIKAFHVFKLFAANQNRPFDIITVLVANRSKLLRFLA

Parental  DFKIDKEDEQFEADKAQIVKEIAALEPRE
          DFK.DKEDE.FEADKAQ..KEI.AL.PR.
Retrocopy DFKTDKEDECFEADKAQVMKEIVALDPRD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Populus trichocarpa was not studied using RNA-Seq expression data.

ChIP-Seq

Populus trichocarpa was not studied using ChIP-Seq data.

EST

Populus trichocarpa was not studied using EST data.

TSS

Populus trichocarpa was not studied using FANTOM5 data.

Lab

retro_ptri_1 was not experimentally validated.

Homology

Retrocopy orthology:

Populus trichocarpa does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G47540	1 retrocopy	retro_atha_11,
Brassica rapa	Bra022139	1 retrocopy	retro_brap_1,
Populus trichocarpa	POPTR_0006s01590	1 retrocopy	retro_ptri_1 ,
Arabidopsis lyrata	scaffold_800035.1	1 retrocopy	retro_alyr_20,